TOol for Motif TO Motif comparison (TOMTOM)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

If you use TOMTOM in your research, please cite the following paper:
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.

Query Motifs  |  Target Databases  |  Matches  |  Program information  |  Explanation

Query Motifs

 Next Top

Name 

Preview 

Matches 

List 

h1v10mes-k27ac-1_h_k27ac-mes_0.589
GAGATAAG
12 Gata1_MA0035.2_J,  Tal1::Gata1_MA0140.1_J,  GATA2_02_M00348_T,  GATA2_03_M00349_T,  GATA3_02_M00350_T,  GATA_Q6_M00789_T,  Gata6_primary_SCI09_U,  Gata3_primary_SCI09_U,  GATA1_04_M00128_T,  GATA1_06_M00347_T
mes15-k27ac-2_h_1_0.559
GACAGATAAG
19 Tal1::Gata1_MA0140.1_J,  Gata1_MA0035.2_J,  Gata6_primary_SCI09_U,  GATA2_02_M00348_T,  GATA1_04_M00128_T,  GATA_Q6_M00789_T,  GATA2_03_M00349_T,  GATA3_02_M00350_T,  GATA4_monomeric_0_P,  Gata3_primary_SCI09_U
mes17-k27ac-3_h_k27ac_1_0.579
CTTATCTGAC
9 Tal1::Gata1_MA0140.1_J,  Gata1_MA0035.2_J,  GATA1_04_M00128_T,  GATA2_02_M00348_T,  GATA2_03_M00349_T,  Gata6_primary_SCI09_U,  Gata3_primary_SCI09_U,  SIRT6_01_M01797_T,  GATA3_02_M00350_T
mes20-k27ac-20_h_1_0.579
CTTATCTG
4 Gata1_MA0035.2_J,  Tal1::Gata1_MA0140.1_J,  GATA1_06_M00347_T,  GATA2_02_M00348_T

Target Databases

 Previous Next Top

Database 

Number of Motifs 

Motifs Matched 

trnsfcJsprUnprobHpdiTaipaleCmbned.meme 3764 19

Matches to Query: h1v10mes-k27ac-1_h_k27ac-mes_0.589

 Previous Next Top

Summary 

Alignment 

Name Gata1_MA0035.2_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.54551e-08
E-value 5.81731e-05
q-value 8.29135e-05
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Tal1::Gata1_MA0140.1_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.20674e-08
E-value 8.30617e-05
q-value 8.29135e-05
Overlap 8
Offset 10
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_02_M00348_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.65991e-08
E-value 0.000137759
q-value 9.16755e-05
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_03_M00349_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.63296e-07
E-value 0.00174385
q-value 0.000870368
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA3_02_M00350_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 8.78745e-07
E-value 0.0033076
q-value 0.00132068
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA_Q6_M00789_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.38771e-06
E-value 0.0127513
q-value 0.00424286
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata6_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.15537e-06
E-value 0.0194048
q-value 0.00552408
Overlap 8
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata3_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.88092e-06
E-value 0.0221358
q-value 0.00552408
Overlap 8
Offset 6
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA1_04_M00128_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.3992e-05
E-value 0.052666
q-value 0.0113346
Overlap 8
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA1_06_M00347_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.50835e-05
E-value 0.0567743
q-value 0.0113346
Overlap 8
Offset 1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA3_monomeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.49967e-05
E-value 0.0940876
q-value 0.0150341
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA4_monomeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.49967e-05
E-value 0.0940876
q-value 0.0150341
Overlap 7
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: mes15-k27ac-2_h_1_0.559

 Previous Next Top

Summary 

Alignment 

Name Tal1::Gata1_MA0140.1_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.1029e-14
E-value 1.16793e-10
q-value 2.33138e-10
Overlap 10
Offset 8
Orientation Normal
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Gata1_MA0035.2_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.37841e-08
E-value 8.95232e-05
q-value 8.93516e-05
Overlap 9
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata6_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.00986e-07
E-value 0.000756511
q-value 0.000444586
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_02_M00348_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.70859e-07
E-value 0.00101951
q-value 0.000444586
Overlap 9
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA1_04_M00128_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.95856e-07
E-value 0.0011136
q-value 0.000444586
Overlap 10
Offset 0
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA_Q6_M00789_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.16094e-06
E-value 0.00436976
q-value 0.00145379
Overlap 7
Offset -3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_03_M00349_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.61758e-06
E-value 0.00985256
q-value 0.00280962
Overlap 9
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA3_02_M00350_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.86253e-06
E-value 0.0145386
q-value 0.00305936
Overlap 9
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA4_monomeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.05815e-06
E-value 0.0152749
q-value 0.00305936
Overlap 7
Offset -3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata3_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.73331e-06
E-value 0.0178162
q-value 0.00305936
Overlap 10
Offset 4
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA3_monomeric_1_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.88613e-06
E-value 0.0183914
q-value 0.00305936
Overlap 7
Offset -3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA5_monomeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.88613e-06
E-value 0.0183914
q-value 0.00305936
Overlap 7
Offset -3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA3_monomeric_0_P
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.87454e-06
E-value 0.0221118
q-value 0.00311016
Overlap 7
Offset -3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gln3_GR09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.96397e-06
E-value 0.0224484
q-value 0.00311016
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata5_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 6.20908e-06
E-value 0.023371
q-value 0.00311016
Overlap 10
Offset 2
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GLN3_01_M01569_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 6.93191e-06
E-value 0.0260917
q-value 0.00325521
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SIRT6_01_M01797_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 8.47188e-06
E-value 0.0318882
q-value 0.00374436
Overlap 7
Offset -3
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name TAL1_01_M01591_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.48404e-05
E-value 0.0558594
q-value 0.0061947
Overlap 9
Offset -1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA1_06_M00347_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.61087e-05
E-value 0.060633
q-value 0.00637019
Overlap 9
Offset -1
Orientation Normal
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: mes17-k27ac-3_h_k27ac_1_0.579

 Previous Next Top

Summary 

Alignment 

Name Tal1::Gata1_MA0140.1_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.05783e-08
E-value 3.98168e-05
q-value 7.9534e-05
Overlap 10
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Gata1_MA0035.2_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 5.89999e-07
E-value 0.00222076
q-value 0.00221798
Overlap 9
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA1_04_M00128_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.39915e-06
E-value 0.00903041
q-value 0.00601275
Overlap 10
Offset 3
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_02_M00348_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 4.48661e-06
E-value 0.0168876
q-value 0.00843324
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_03_M00349_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 7.971e-06
E-value 0.0300029
q-value 0.0112444
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata6_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 8.97331e-06
E-value 0.0337755
q-value 0.0112444
Overlap 10
Offset 5
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name Gata3_primary_SCI09_U
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.631e-05
E-value 0.0613907
q-value 0.017308
Overlap 10
Offset 8
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name SIRT6_01_M01797_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.84162e-05
E-value 0.0693187
q-value 0.017308
Overlap 7
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA3_02_M00350_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.25247e-05
E-value 0.0847829
q-value 0.0188171
Overlap 9
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]

Matches to Query: mes20-k27ac-20_h_1_0.579

 Previous Next Top

Summary 

Alignment 

Name Gata1_MA0035.2_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 3.25087e-06
E-value 0.0122363
q-value 0.0244452
Overlap 8
Offset 2
Orientation Reverse Complement
Create custom LOGO ↧  [Next Match] [Query Top]

Summary 

Alignment 

Name Tal1::Gata1_MA0140.1_J
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 1.57323e-05
E-value 0.0592163
q-value 0.0456507
Overlap 8
Offset 0
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA1_06_M00347_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.24107e-05
E-value 0.0843537
q-value 0.0456507
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Next Match] [Query Top]

Summary 

Alignment 

Name GATA2_02_M00348_T
Database trnsfcJsprUnprobHpdiTaipaleCmbned.meme
p-value 2.42836e-05
E-value 0.0914034
q-value 0.0456507
Overlap 8
Offset 1
Orientation Reverse Complement
Create custom LOGO ↧ [Previous Match] [Query Top]
Previous Next Top
TOMTOM version
4.8.1 (Release date: Tue Feb 7 14:03:40 EST 2012)
Reference
Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble, "Quantifying similarity between motifs", Genome Biology, 8(2):R24, 2007.
Command line summary

Background letter frequencies (from first motif database):
A: 0.295   C: 0.205   G: 0.205   T: 0.295

Result calculation took 11.864 seconds
show model parameters...

Explanation of TOMTOM Results

 Previous Top

The TOMTOM results consist of

Inputs

The important inputs to TOMTOM.

Query Motifs

The query motifs section lists the motifs that were searched for in the target databases as well as links to matches found.

Name
The motif name.
Alt. Name
The alternative motif name. This column may be hidden if no query motifs have an alternate name.
Website
A link to a website which has more information on the motif. This column may be hidden if no query motifs have website information.
Preview
The motif preview. On supporting browsers this will display as a motif logo, otherwise the consensus sequence will be displayed.
Matches
The number of significant matches.
List
Links to the first 20 matches
Target Databases

The target motifs section lists details on the motif databases that were specifed to search.

Database
The database name.
Number of Motifs
The number of motifs read from the motif database minus the number that had to be discarded due to conflicting ids.
Motifs Matched
The number of motifs that had a match with at least one of the query motifs.

Matches

The matches section list the group of motifs that match each query motif. For each query-target match the following information is given:

Summary Table

The summary gives the important statistics about the motif match.

Name
The name of the matched motif.
Alt. Name
The alternative name of the matched motif.
p-value
The probability that the match occurred by random chance according to the null model.
E-value
The expected number of false positives in the matches up to this point.
q-value
The minimum False Discovery Rate required to include the match.
Overlap
The number of letters that overlaped in the optimal alignment.
Offset
The offset of the query motif to the matched motif in the optimal alignment.
Orientation
The orientation of the matched motif that gave the optimal alignment. A value of "normal" means that the matched motif is as it appears in the database otherwise the matched motif has been reverse complemented.
Alignment

The image shows the alignment of the two motifs. The matched motif is shown on the top and the query motif is shown on the bottom.

Create custom LOGO

By clicking the link "Create custom LOGO ↧" a form to make custom logos will be displayed. The download button can then be clicked to generate a motif matching the selected specifications.

Image Type
Two image formats, png and eps, are avaliable. The pixel based portable network graphic (png) format is commonly used on the Internet and the Encapsulated PostScript (eps) format is more suitable for publications that might require scaling.
Error bars
Toggle error bars indicating the confidence of a motif based on the number of sites used in its creation.
SSC
Toggle adding pseudocounts for Small Sample Correction.
Flip
Toggle a full reverse complement of the alignment.
Width
Specify the width of the generated motif.
Height
Specify the height of the generated motif.